No abstract

Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigated the biological relevance of H3K4me3 and H3K27me3 in secondary xylem development using ChIP-seq and their association with transcript levels among other histone modifications in woody and herbaceous models. In developing secondary xylem of the woody model Eucalyptus grandis, H3K4me3 and H3K27me3 genomic spans were distinctly associated with xylogenesis-related processes, with (late) lignification pathways enriched for putative bivalent domains, but not early secondary cell wall polysaccharide deposition. H3K27me3-occupied genes, of which 753 (~31%) are novel targets, were enriched for transcriptional regulation and flower development and had significant preferential expression in roots. Linear regression models of the ChIP-seq profiles predicted ~50% of transcript abundance measured with strand-specific RNA-seq, confirmed in a parallel analysis in Arabidopsis where integration of seven additional histone modifications each contributed smaller proportions of unique information to the predictive models. This study uncovers the biological importance of histone modification antagonism and genomic span in xylogenesis and quantifies for the first time the relative correlations of histone modifications with transcript abundance in plants.

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The Botryosphaeriaceae are common and diverse members of fungal communities infecting woody plants. They are also increasingly being used as model organisms to understand patterns in the global movement of latent pathogens. The aim of this study was to consider the species richness of the Botryosphaeriaceae associated with the native Acacia (Vachellia) karroo across South Africa, and the variation of species at specific local sites over time. The diversity of these fungi associated with different tissues of this host plant was also considered. These questions were addressed by sampling healthy A. karroo from 23 sites in South Africa and by more intensive hierarchical sampling conducted at 40 sites in one area over 3 yr. In total, 13 species of the Botryosphaeriaceae were identified, including seven that were isolated only from the more intensively sampled area. There was a clear geographical influence, with some species occurring only in some parts of the country. Significant variation in the species richness over time for the intensively sampled area was found and there was no evidence of tissue specificity for this group of fungi in leaves, branches and branchlets. Results of pathogenicity trials showed highly variable lesion sizes for the isolated species in comparison to the control, with Sphaeropsis variabilis, Lasiodiplodia theobromae and Neofusicoccum australe being the most pathogenic. The overall results revealed a rich diversity of Botryosphaeriaceae on this native host, which varied significantly both geographically and on individual trees, even in the absence of obvious disease.

A Hill-type time-response curve was derived using a single-step chemical kinetics approximation. The rate expression for the transformation is a differential equation that provides an interpolation formula between the logistic growth curve and second order kinetics. The solution is equivalent to the log-logistic cumulative distribution function with the time constant expressed in terms of a kinetic rate constant. This expression was extended to a full dose-time-response equation by postulating a concentration dependence for the rate constant. This was achieved by invoking a modified form of Haber’s law that connects an observed toxic effect with the concentration of the active agent and the elapsed exposure time. Analysis showed that the concept of Concentration Addition corresponds to a special case where the rate constant for the overall transformation rate is proportional to the sum of the rate constants that apply when the agents act individually. Biodiesel “survival” curves were measured and used to test the applicability of the empirical model to describe the effects of inhibitor dosage and binary inhibitor mixtures. Positive results suggest that the proposed dose-response relationship for the toxicity of agents to organisms can be extended to inanimate systems especially in cases where accurate mechanistic models are lacking.